Hi, here is what I have done:
First, I set up the distribution for a state, then do
siteDistribution.setNullModel(nullDistribution);
to set up the null Distribution
then use this function to get the odds ratio of my C3 state (the one i
am interested in). Maybe I can try getting the odds ratio for the
background state and see what numers I got?
public static void getC3PosteriorOdds(MarkovModel model, SymbolList
obsSymList) throws IllegalArgumentException, BioException {
DP dp = DPFactory.DEFAULT.createDP(model);
SymbolList[] obs_array = {obsSymList};
DPMatrix dpMatrix = dp.forwardsBackwards(obs_array,
ScoreType.ODDS);
State [] states = dp.getStates();
//find the C3 site
int c3Index = -1;
for (int s = 0; s < dp.getDotStatesIndex(); s++) {
if (states[s].getName().equalsIgnoreCase("C.3")) {
c3Index = s;
break;
}
}
for (int i = 0; i < obsSymList.length(); i++) {
int[] array = { c3Index, i };
log.debug(i+1 + " " + dpMatrix.getCell(array));
}
}
thanks,
wendy
On 3/6/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> >Hi,
> >
> >I am trying to set up an HMM wth a few states. I have a background
> >state with background distribution. For the rest of the states, I set
> >up the distribution and then use the setNullModel to set the null
> >distribution to the background distribution. Am I doing the right
> >thing?
>
> Sounds correct.
>
> >The reason why I am asking is when I tried using the forward backward
> >algorithm, the scores of the state that I am interested in at each
> >site is greater than 2000. I would expect some sites to have a number
> >less than 1 to indicate that it is more likely to be in the null
> >distribution, or am I doing something totally wrong here?
>
> If you used an odds scoring function then you have done things correctly.
> Sounds wierd.
>
> - Mark
>
>
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